The Ministry for Primary Industries (MPI) is rejecting the wine sector's claim that it will get a raw deal in proposed primary sector price hikes.
MPI was looking at upping fees for its food safety service by 12 percent, and biosecurity work by 20 percent, as part of a review of its work.
It would be the first review of fees to support the biosecurity system since MPI was formed in 2011 and would be the first review of food safety fees since 2008.
But the wine industry has voiced its opposition to paying $2.9 million more a year, on top of the $200 million it pays now to meet the costs of MPI's wine regulatory programme.
Winegrowers New Zealand chair Steve Green said it meant the wine industry would be unfairly hit.
"We are different from the other primary sectors that are being approached because we pay excise, those excise go directly into the Government's coffers.
"That is a huge tax that we pay that no one else is paying."
Mr Green said wine exports topped $1.3 billion last year and the Government should be supporting growth, not imposing taxes.
But the Ministry's deputy director-general Dan Bolger said the wine sector fees were set when it was a much smaller industry than it was now.
He said the proposed increase put winegrowers on par with other primary sector businesses.
Mr Bolger said the review came on the back of higher demand for the Ministry's services.
He said exports would never make it overseas if MPI did not maintain food and biosecurity standards in New Zealand.